GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylF_Tm in Tistlia consotensis USBA 355

Align ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized)
to candidate WP_085121058.1 B9O00_RS01465 ABC transporter permease

Query= TCDB::Q9WXW7
         (317 letters)



>NCBI__GCF_900177295.1:WP_085121058.1
          Length = 335

 Score =  169 bits (427), Expect = 1e-46
 Identities = 107/304 (35%), Positives = 169/304 (55%), Gaps = 3/304 (0%)

Query: 9   TFRELGPLVALVSLAVFTAILNPRFLTAFNLQALGRQIAIFGLLAIGETFVIISGGGAID 68
           T  EL  L   + +    ++L+P FLT  N+  +  Q  + G+L+IG TFVI++GG  ID
Sbjct: 30  TSLELRMLGLALVIGAVLSLLSPYFLTESNIFNILDQSVVIGILSIGMTFVILTGG--ID 87

Query: 69  LSPGSMVALTGVMVAWLMTHGVPVWISVILILLFSIGAGAWHGLFVTKLRVPAFIITLGT 128
           LS GS+  L+G+++  L     P+ ++++L +L   G G   G+ +   R+ AF++TLG 
Sbjct: 88  LSVGSVAGLSGIVLG-LALKDYPIPVAILLGVLTGAGVGLVSGILIGYFRLAAFVVTLGM 146

Query: 129 LTIARGMAAVITKGWPIIGLPSSFLKIGQGEFLKIPIPVWILLAVALVADFFLRKTVYGK 188
           + I R +A + +    I G PS    I   +   IP  V  L    L+A  +L  T  G+
Sbjct: 147 MAIGRSLAYIFSGQTAISGFPSDLSSIVYTDVFGIPTNVLFLGFAYLLAWGYLTYTKGGR 206

Query: 189 HLRASGGNEVAARFSGVNVDRVRMIAFMVSGFLAGVVGIIIAARLSQGQPGVGSMYELYA 248
            + A G N+ AAR +G+ V    ++ ++VSG LA V      A++    P  G+  EL A
Sbjct: 207 TIYAIGSNKEAARAAGLGVLFYSILPYVVSGALAAVAITFSVAQILSVDPLTGNGMELDA 266

Query: 249 IASTVIGGTSLTGGEGSVLGAIVGASIISLLWNALVLLNVSTYWHNVVIGIVIVVAVTLD 308
           IA+ VIGG SL GG GS++G ++G  I+ ++ N L LL VS +W    IG +I++A+ ++
Sbjct: 267 IAAVVIGGASLYGGRGSIVGTLIGVLIMVMIRNGLNLLGVSPFWQGSAIGSIIIMALLVE 326

Query: 309 ILRR 312
            L R
Sbjct: 327 RLVR 330


Lambda     K      H
   0.328    0.143    0.424 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 337
Number of extensions: 25
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 317
Length of database: 335
Length adjustment: 28
Effective length of query: 289
Effective length of database: 307
Effective search space:    88723
Effective search space used:    88723
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory